Quantum Entanglement
by BrekkanTheRules
Summary: John Watson is asked to help with some experimentation by Sebastian Moran. What originally sounds harmless, is soon discovered to be human experimentation. John needs to do what he can to help the victim, a genius named Sherlock Holmes, before something even worse happens.
1. Chapter 1

_Quantum Entanglement enables particles to affect each other instantaneously across any distance. Entangled particles would remain connected even if they were on opposite sides of the universe._

xxx

John Watson slowly limped his way down the sidewalk, one hand tightly gripping his cane, and the other carrying a shopping bag full of medical textbooks. Thinking back on it, he really should have double-bagged the books, as he could feel the plastic starting to give way. He sighed and thought about turning back and heading home. It was dreadfully cold, and he would much rather spend his evening sitting in front of a roaring fire, than lending his knowledge to an old classmate who was always a bit of an arse.

When John was in his last few years of secondary, he had his whole life planned out. He knew he wanted to be a doctor, and he wanted to join the army. He was quite vocal about his plans, so anyone who knew him then knew what he would become. After his return from the army, John could probably count on one hand how many of his classmates from that time he'd seen, but there was one who kept popping up.

Sebastian Moran wasn't the type of person John spent any time with at school. He was a bully, always using his size to his advantage, and John wanted nothing to do with him. Not that Sebastian ever showed an interest in being John's friend either. They both happily and successfully stayed out of each other's orbits for their school careers, and frankly John had forgotten all about him.

A few weeks after being invalided back to London, John was reluctantly doing a bit of shopping when he heard his name called through the crowd. He turned and scanned for a familiar face, the person who yelled his name, but he couldn't pick anyone out. None of these people could know his name. As he was returning to his business, he saw a stocky blond elbow his way through the crowd. John raised an eyebrow. Was this the voice he'd heard? Who was this guy? And how did he now John's name?

"You don't remember me, do you, Watson?" the blond had a smirk on his face, and was clearly amused at John's confused expression.

"No, should I?" John was in a bit of a strop already, transitioning back to civilian life wasn't easy. "Sorry," he added, somewhat belatedly.

The man chuckled, obviously not offended by John's brusque reply. "Sebastian Moran. We went to school together."

"Oh, right. Good. How are things, then?"

"Good, thanks. I figured you'd be overseas by now, getting shot at for Queen and Country," Moran's tone was condescending but John wasn't in the mood to set him straight.

"Yep," John replied blandly, just wanting the conversation to end. "I got shot."

xxx

The next time John encountered Moran, he was sitting in a remarkably empty train carriage. He'd been held late at the surgery, so it had been hours since rush hour had finished on the tube. While he was exhausted from the extra hours, he was quite happy to not have the unpleasant feeling of being one of many sardines stuffed into a can.

He was sitting quietly absentmindedly rubbing his sore leg that hadn't sustained any injury, and so didn't notice immediately that someone had sat beside him.

"Didn't expect to run into you here, Watson!" Moran's voice was loud and echoed off the metal walls of the carriage. John forced a smile at him, wishing he was in his bed, sleeping.

"You're a doctor, is that right?" Moran didn't seem to be asking condescendingly so John nodded, briefly explaining that while he couldn't do surgery anymore, he was still working as a GP. Moran actually seemed interested, and spent the rest of the trip asking John questions about what he'd encountered as a doctor, the typical stuff as well as the weird and wonderful. John actually found himself enjoying the conversation, it was nice to talk about his accomplishments as a doctor without bringing up the war.

As the train slowed at John's station, Moran thanked John for the pleasant conversation. "Maybe I'll see you again soon," he chuckled right before the doors closed, leaving John at the station.

xxx

There was a light knock against the door of John's office, and his boss Sarah popped her head in.

"Sorry to bother you, John, but there's a man here to see you. He says he knows you and wanted to speak to you."

John checked to see if he had any appointments coming up, then asked Sarah to bring him in. He scratched his head as he waited, assuming it was Moran and confused as to why he'd drop in at the surgery. While they'd run into each other a few times since the train, he wouldn't consider them friends that dropped in on each other.

Sarah knocked again before leading Sebastian in, and taking her leave. Sebastian dropped into the seat reserved for John's patients and rubbed his forehead with his hand.

"Watson, I've got something to ask you. You know your stuff when it comes to medicine, and right now I need someone like you."

John was confused to say the least, as it suddenly occurred to him that he'd never even asked Moran what he did for a living. "Need someone like me for what?" John asked, careful not to agree to anything with no knowledge.

"I do some work for this guy, right? He's a proper genius. Got a lot of huge ideas in his brain, and it's up to me to help him make those ideas into reality. Normally it's easy enough, but this time it's a bit above my pay grade. I was shit at biology in school, so that's why I'm asking you."

John sat silently and waited for him to continue. He watched as Moran began to fidget, tapping out a beat with his fingers on his knee.

"Do you know much about DNA splicing, John?"

The question caught him off guard. It wasn't a topic that John would have ever guessed Moran would know about, let alone discuss. He shook his head slowly.

"No, not really. I know enough about DNA in general, but splicing is out of my depth."

Moran sighed in response. "What if I said I have tons of information on splicing, but I can't make heads or tails of it? Could you understand it?"

John blanched. "What are you asking me, Sebastian?"

He sighed again before leaning forward in his chair and resting his elbows on his knees. "I guess what I'm asking is... Look. My boss wants to try his hand at splicing. Thinks he can use it to benefit the meat industry, don't ask me how. That's not my area. My job is to get it done. I had a professional in, and he was great. Really making progress. But he got mixed up in some seedy stuff in his regular life and he's been locked up. Domestic abuse, I think. Anyway, now I've got a load of records he kept, but no way to continue the work. So I guess that's what I'm asking. I have all of his work, and it's mostly finished, but I need someone to complete it. A couple weeks worth of work, that's all. I figured that with your medical knowledge, and his notes, it might be possible. I know I'm asking a lot, but I'm at a loss. I'd be able to pay you, of course. Quite a bit."

John blinked. Once, twice, three times. Then he sighed, "I can't make any promises. Even with the notes it could be out of my depth."

Moran's eyes widened and his face showed his hopefulness. He jumped up out of his chair and leaned over the desk towards John. "Of course, John, of course! It would mean a lot that you'd even try! You'll do it?"

John mentally kicked himself but nodded anyway. He could use the extra money, at any rate. "I'll give it a shot."

xxx

Moran had written down an address as he thanked John for the tenth time before running out of the office. John scooped the address out of his pocket and squinted at the street sign ahead of him. Baker Street. Glancing down the street he saw a tall black door with a shiny gold address affixed to the front. 221B.

He limped to the door and slowly reached his hand towards the heavy door knocker. He steeled himself and knocked.

What had he gotten himself into?

xxx

 _Please leave me reviews, they keep me warm. This fic will be eventual johnlock since I'll go down with this ship. I know there's an upsetting lack of Sherlock in this chapter, but I will fix that in the near future (like as in the next chapter)_ _Thanks for reading!_


	2. Chapter 2

Sebastian Moran ushered John inside with a manic grin on his face. He led John up a flight of stairs while murmuring about how pleased he was that John would be helping. He opened the door at the top of the stairs and John was surprised to see that it looked like a normal flat.

He'd been expecting some sort of medical lab, but maybe a bit more technologically advanced than the labs he'd spent time in. What he saw instead was a typical flat, complete with a sofa, fireplace, and a weird cow skull on the wall. Were those headphones?

Moran had moved to the kitchen, looming over the dining table that was littered with science equipment. John stepped into the kitchen and realized they'd turned it into a makeshift lab. Every flat surface was covered with equipment or files, and the walls were littered with notes stuck to it.

"Right. Here's the bloke's notes. I'm gonna let you handle them since they're rubbish to me. Think of this area as your base of operations. The loo is just down that hall a bit. Sorry, I've gotta dash, the boss is making demands again." He winked conspiratorially at John, as though they had both shared a little joke. Moran clapped him on the shoulder as he left. "Thanks for doing this, mate. Your assistant will be here shortly."

John heard the loud bang of the closing door and dropped into the nearest chair, sighing. With one hand he grabbed the file, while the other scrubbed his face as he asked himself for the hundredth time why he'd agreed to this. Because you need something, his brain helpfully supplied. You need something interesting to happen to you.

He flipped open the file as he murmured aloud "nothing happens to me."

xxx

John was so immersed in the scientist's notes that he didn't hear the door to 221B click open. He was too busy trying to wrap his head around the idea of modifying a creature's DNA in a way that made the creature better without any devastating or fatal side effects. He couldn't help but shudder at the idea of getting it wrong.

"Oh!" came a soft voice from the doorway, and the loud thud of an object being dropped to the floor. John jumped out of his chair, wincing at his leg, and quickly assessed the new arrival.

She was a soft, mousy woman. Her face was kind as she bent over and scrambled to pick up the items she'd dropped in her surprise. John wobbled over to help her.

"Thanks," she said quietly as John handed her the last can of diced tomatoes. "You must be Doctor Watson." It wasn't a question so much as a statement. She refused to meet John's eyes as she turned from him and ventured into the kitchen. John followed and watched as she emptied her grocery bags into the fridge. He'd honestly assumed the fridge was for experiments, not actual food. She turned back to him, still not meeting his gaze, and sighed. "I'm Molly Hooper. I... I wasn't expecting you to be here yet." She turned from him again and began rooting in cupboards, pulling out a few pots and dishes. "Doctor Magnussen was always late," she spoke over her shoulder as she filled the pot with water before placing it on the stove.

John watched her as she quickly made a large batch of spaghetti and spooned it onto 3 plates. She motioned to the table and he sat down slowly as she placed a plate in front of him and sat down with her own.

She seemed content to eat in silence, but John was feeling rather awkward about the whole encounter and wanted to make a better first impression.

"Call me John. I, uh, don't feel like much of a doctor anymore." He rubbed the back of his neck and continued to eat. Out of his peripheral vision he saw her finally looking at him. He didn't want to interrupt her by returning the gesture, so he continued to stare at his plate.

"Right. John, then. How did you wind up here, John?"

xxx

After their meals, Molly placed the two empty plates in the sink, and John suddenly remembered the third plate. It was still sitting on the counter, untouched. He wondered if she had just made too much, and maybe she'd put it in the fridge for leftovers. Molly was fussing about the kitchen and didn't take any mind of the third plate, so John figured he was spending entirely too much time worrying about it, when he should be more focused on the notes.

He returned to the armchair in the living room that he'd already branded as his own, and delved into the files again.

Now and again he'd hear sounds from Molly as she cleaned up. A clink as she moved dishes in the sink, a scrape as she moved a piece of equipment across the countertop. It all felt rather domestic and it helped John to relax a bit.

After a few minutes, (or was it an hour?) John looked up from the notes to ask Molly how much she knew about the splicing, and whether she thought it was particularly ethical. When he didn't get a response he moved to the kitchen to ask again.

The kitchen was empty. He shrugged his shoulders, assuming Molly had run to the loo or something. He turned back to his chair but out of the corner of his eye he saw the countertop. The empty countertop, with no sign of the extra spaghetti plate.

Maybe she'd put it away. For some inexplicable reason, he checked the fridge for the leftovers, but found none. He moved to the sink and saw just the two empty plates and their cutlery.

That was odd. Was it odd? Why was it odd? Where was the extra spaghetti?

xxx

Molly returned to the flat not long after, defeat clearly written on her face. In her hand, she held the spaghetti plate. She moved to the kitchen, seemingly unaware that John was watching her, and scraped the remaining spaghetti into the bin. John noticed that there was almost the same amount of spaghetti on the plate that she'd originally dished up.

"Molly," John spoke and she jumped, flinging the empty plate into the sink with a loud clink. "What is your job here?"

"Oh, I just helped Doctor Magnussen when he needed me. I was his assistant."

John looked back at the notes in his hand. "These notes talk of practical research. Not just theory, but the results of live experiments. Why is our lab in central London, when we should really be at a farm to conduct these experiments?"

"Farm?" Molly's face was a stoic mask. "We go to the farm when we need to see how the theory works in practice. We don't need to be there all the time. In fact, you probably won't go at all. We just need you to finish the latest theory, and we'll test it ourselves."

"Without me? What if my theory is bollocks? It would make sense for me to test my own theory, so I could make changes where..." he trailed off when he saw the mask on Molly's face slip. It was just for a second, he wouldn't have noticed if he'd looked at her a fraction of a second later. For a brief moment, her face was pained. As though she was physically hurting. Then the calm mask returned and she sighed.

"I don't decide these things, John. Just... Just do your job and I'll do mine." She turned back to the sink and began scrubbing the dishes.

John reluctantly returned to his notes.

xxx

" _Now, it's come to my attention that jellyfish has a type of immortality in that they do not age and will not die of natural causes. Naturally, they can be killed, but that is something for another day. Think how wonderful it would be if we humans were able to absorb that trait from jellyfish. Sure, people would still be killed, but we wouldn't lose great minds from nuisances like old age. Excellent. I've managed to isolate the gene and it must be administered to the patient over a period of time."_

John didn't like the way the words on the page made his skin crawl. He supposed it would be helpful if accidents couldn't happen to cattle, causing a shortage of meat, but it seemed extreme to discuss applying the trait to humans.

He shook his head and glanced around the flat. The lights were on, but they were dim. The whole place was warmly lit by just a couple bulbs, adding an ominous feel to the room. He glanced at the fireplace, maybe he should light it? It would add more warm light to the room, and might chase off the shivers running down his spine.

He got up from his chair and knelt down, piling on a few logs from the nearby pile. A bright streak of white in the ash caught his attention. Paper. Paper that someone had tried to burn. He fished it out and thankfully, it was mostly intact. He leaned back on his heels and began to read.

 _"Day 1: obviously no notable reaction. I expected this. We cannot create perfection overnight._ _Day 12: subject has been violent. Understandable. Altering genetic makeup can't be comfortable. Still, we press on. No immediate negative side effects._ _Day 35: subject is refusing food. Yet, it does not seem like a wish to die. The subject simply doesn't require food? Worth further study._ _Day 51: found another gene, this time from a raven, that I hope will ramp up intelligence. While the subject is not dim-witted, by any means, the subject can be better. Smarter. Perfect. I've begun treatments with this gene as well._ _Day 55: the raven gene is showing a quicker reaction than the jellyfish. The subject is already showing a heightened level of intelligence. Incredible._ _Day 75: this is it. I am so close to perfection. We've spliced some of the greatest genes into the subject, now we only need time. Time for the genes to fully take effect, so we need to continue treatment for just a little longer. Sadly, I fear for my work. They're on to me. I've spoken to Jim but he doesn't seem worried. He asked if my work was done, and I told him yes, the difficult part is done but treatments need to continue for another week, at least. I regret telling him that. I am no longer required. The weak-willed woman can do the job now. Unless I sabotage the last treatment. She isn't skilled enough to create the treatment, only administer it. I hate to leave the experiment unfinished, but I fear for my life unless I am required. I've written in the notes that my final treatment was a dud and that I need to rework the formula. They will need me._ _Day 76: I've been instructed to leave Baker Street. Jim said there was nothing they could do to stop Scotland Yard. I can't be caught here. If they catch me here they'll search the whole place and they'll find him. If they find him, my life is as good as over. They won't understand. I hid the treatment in the house. They'll never find it. I'll return and finish what I've started."_

"Molly," John somehow managed to keep his voice steady and calm. Steady and calm. Breathe in, breathe out. Calm. He heard the muffled footsteps as Molly stepped into the living room from the kitchen. He turned to her and her gaze snapped to the burnt paper in his hand. Her hand rose to her mouth. "Where is he?"

He didn't quite manage to keep the rage out of his voice.

xxx

 _Sorry for the long chapter but it kinda ran away from me! I know nothing about genes or splicing, I just messed around with some ideas that are probably completely incorrect but hey, it's fiction. Please review! I promise Sherlock in the next chapter._


	3. Chapter 3

Molly led John out of the small flat, and up a dark set of stairs just outside the door that John didn't notice when he arrived. John was shaking, rage flowing through him at the idea of someone experimenting on a human. A human being! Not to mention how unethical it was to experiment on people, he didn't know how someone could actually stomach physically doing it. What kind of a person could do that?

It vaguely registered in his head that he should be limping up these stairs, but his legs were perfectly steady. Odd. He'd have to think about that later. Sometime after he figured out how to get the human science experiment out of this horrendous place.

As Molly slowly walked ahead of him down a dark hallway at the top of the stairs, he noticed that she was tapping the wall. No, not just tapping. Tapping and scraping with her nail. Scrape, scrape. Scrape, scrape, scrape. Tap, scrape, tap, tap. He listened carefully.

Morse code. She was tapping out Morse code on the wall. It was simple Morse, just her name, over and over. Molly, Molly, Molly.

She stopped dead at a darkly painted door. This whole area was painted darkly, in a way that you probably wouldn't notice it if you weren't looking for it. John shuddered at the implications of that.

"It's me. It's only me," she whispered at the door before slowly turning the knob. John noticed she was holding her breath.

xxx

As Molly led John through the door, he looked around him in awe. The walls were covered in fabric, probably to muffle any sound from the room, and the whole place was brightly lit with industrial strebgth fluorescent tubes. In the middle of the room was a floor-to-ceiling glass wall. He and Molly were on one side, and on the other side sat a figure facing away from them. DO NOT TOUCH THE GLASS was etched into the wall ominously.

"I'm not in the mood," came a long, deep drawl from the figure, although he didn't turn to face them. The voice was hoarse from lack of use. "Leave me."

Molly dropped to her knees and leaned her palms and forehead against the glass, whispering and mumbling too low for John to hear. John ignored her and looked back at the figure.

He was shirtless, and his black pants looked torn and dirty. His black hair hung damp and limp on his head. It wasn't very long, they must cut it sometimes. John could see his ribs easily through the almost translucent white flesh and his jaw tightened. They didn't even have the decency to feed this man?

"You didn't notice the extra plate?"

John was startled out of his once-over by this man apparently reading his thoughts and responding to them.

"I... I'm sorry?" John stuttered.

"The extra spaghetti," Molly spoke quietly, still leaning her forehead against the glass. "I knew you noticed it. I brought it up to him. I always do. He won't eat."

Molly sounded so broken that John held back his urge to laugh in her face. Instead, he calmly spoke his thoughts.

"Why should he eat it? After what you've done..."

He placed a palm on the glass and the figure inside turned to face him.

John wasn't prepared for the sheer physical presence of the man behind the glass. His eyes almost glowed from behind the fringe of his hair, their blue was unnatural and piercing. Instead of being a weak, fragile specimen, in that moment he seemed powerful, unwavering and severe. The sharpness of his gaze struck John to his core.

The man walked slowly, very slowly, up to the glass separating them.

"Have you come to finish the job, Doctor? Only one treatment left. Only one... But that's not right. That's not why you're here," his head cocked to the side and his eyes narrowed as he searched John with his gaze. "They lied to you. They didn't tell you about me. You didn't know... Well now you do. Will you finish it?"

The man's severity seemed to push through the glass and John had to step back. The man wasn't deterred, he stepped ever closer, almost flush against the glass, and whispered "well, doctor?" with a menacing, wild grin on his face.

Molly sobbed from her spot on the floor. "Sherlock, I told you, I destroyed it. He... He can't finish it even if he wants to."

John looked down at her, confused. "Molly how could you allow this?"

The man, Sherlock, spoke again. "The fault isn't with Molly. She's only done as I asked."

xxx

John was sitting at a large metal table that looked like an operating table with his head in his hands as Molly explained.

 _Sherlock Holmes, consulting detective had come up against his toughest nemesis. Jim Moriarty was always two steps ahead. He knew too much about Sherlock, knew how to use his weaknesses against him. Unfortunately for both of them, Sherlock didn't have many weaknesses. So Jim had to improvise. Capturing Sherlock was difficult, many months and weeks of planning, but it was successful._ _Jim didn't think it would be enough to just kill Sherlock. He wanted to break him. Alter him. Destroy him. So the experiments started._ _Jim hadn't expected Molly since Sherlock didn't have friends. Molly was left subtle clues by Sherlock days before his capture, and she was smart enough to locate him. With her medical skills she got placed on the team of Dr Magnussen, and was able to personally see Sherlock._ _She was at a loss how to proceed, though. She could see Sherlock, was able to be with him through the toughest moments. The excruciating pain and the unbearable weakness. She couldn't work out a way to get him out._ _It was made clear that Jim was able to destroy the whole flat at the touch of a button, and she hadn't been able to work past that._ _Magnussen getting caught had been a stroke of good luck, since the experiment would have to be put on hold until a replacement was found. Molly had found the final treatment and replaced it with saline solution_ _Then Moran had arrived and told Molly about the replacement, and that the experiment would continue. The last thing Moran had said to her was "whatever happens, John can't know about Sherlock. He's... weak-willed. He can't handle it like we can. He just needs to finish work on the treatment and you will take it from there."_

xxx

"You see now," Sherlock's voice was steady on the other side of the glass, "why Molly did what she did. She's the strongest person I know. She did it out of kindness to me."

Molly let out a shaky sigh across the table from John.

"As for you, doctor, you've invaded Afghanistan. This can't be much more difficult."

"John," the doctor croaked, his face still buried in his hands. "Call me John."

 _Thanks for reading! Reviews make me happy. I'm also extremely sick and have a low-lying fever so forgive me if this makes very little sense!_


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